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The big new cholesterol-lowering drug from Genzyme and Isis Pharmaceuticals, which both companies are counting on as a future profit driver, passed its first major clinical trial, but investors didn’t like what they saw when full details were released this morning at a major medical meeting.

Carlsbad, CA-based Isis Pharmaceuticals (NASDAQ: ISIS) fell 16 percent to $11.17 at 1:30 pm Eastern time after details from the trial of the drug, mipomersen, were released at the American Heart Association’s scientific sessions in Orlando, FL. Cambridge, MA-based Genzyme (NASDAQ: GENZ), which isn’t nearly as dependent on the drug, saw its shares climb 2.6 percent.

Expectations have been running high for this drug for years, with many seeing it as the next big thing for cholesterol after the invention of multi-billion dollar statin drugs such as Pfizer’s atorvastatin (Lipitor). Isis’ very bullish CEO Stanley Crooke told me last month that the drug represents an historic advance. The drug is thought to have promise because it is the first of its class that’s made of specially engineered strands of RNA drugs to block a problematic protein in the body, which often can’t be hit by conventional small-molecule drugs. In this case, mipomersen is engineered to block the production of a protein called apoB that carries the so-called “bad” LDL cholesterol in the bloodstream. The drug is originally being tested among patients with a one-in-a-million genetic condition that causes them to die young from their extremely high cholesterol, although Genzyme and Isis envision this drug becoming more widely used among wider populations of people with extremely high cholesterol that can’t be controlled by existing meds.

“Mipomersen may well be a valuable addition to the therapeutic armamentarium,” said Frederick Raal, the primary investigator of the pivotal study of mipomersen, during a webcast from today’s scientific meeting. Raal is the director of the Carbohydrate and Lipid Metabolism Research Unit at the University of the Witwatersrand in South Africa.

So what was in the data that made Isis investors, at least, skittish? First off, it should be noted that the headline results were released back in May, when Isis and Genzyme said that mipomersen reached its goal of lowering “bad” LDL cholesterol by 25 percent, compared with a 3 percent reduction on placebo, in a study of 51 patients with homozygous familial hypercholesterolemia. This meant that patients had a 100 milligram per deciliter drop in their LDL scores, which significantly lowers their risk of dangerous cardiovascular events like heart disease and stroke, Raal said. Isis and Genzyme added further detail on the effect at today’s meeting, essentially showing that secondary goals, such as lowering total cholesterol and triglycerides, also were achieved among patients on the drug.

But the treatment, which was given in a once-weekly 200 milligram injection, had some side effects worth noting. Four of the 34 patients $12 percent) who were treated with mipomersen had elevations in liver enzymes that were triple normal levels, which can be an indicator of liver damage. Six of the 34 mipomersen patients (18 percent) dropped out of the study, including two for swelling around their injection sites, one for the elevated liver enzymes, one for rash, one for personal reasons, and another for non-compliance with study protocol.

Raal, in his comments to investors during today’s webcast, noted that it’s common to see increases in liver enzymes in patients taking cholesterol-lowering drugs. No patients had their liver enzymes run so high that they were classified at high risk under something called Hy’s Law. That’s a severe condition in which drugs damage the liver, which leads to jaundice and without a liver transplant can be fatal in 10 to 50 percent of cases, according to this Wikipedia entry.

“All lipid-lowering drugs are associated with” elevated liver enzymes, Raal said during a question-and-answer session with analysts. “We in this field see it almost as the liver turning up its thermostat.” He said that he’s never seen liver enzymes rise high enough to turn into a severe case like those classified by Hy’s Law. “This isn’t a scary thing,” Raal said.

Still, it’s obviously a black mark for a drug to have doctors even thinking about that much potential liver damage, so it’s no surprise that Isis and Genzyme are backing off on the dose of mipomersen in some future trials. Two new studies are being planned to look at different doses and schedules, including one that will compare a 30 milligram daily shot, a 70 milligram three-times-weekly injection, and the 200 milligram weekly dose that was used in this first pivotal trial.

Genzyme also says it is still refining its game plan for how to get approval of mipomersen in the U.S. and Europe. The company plans to file its application with regulators in the U.S. and Europe in mid-2011. That represents a bit of a delay, according to Leerink Swann analyst Joseph Schwartz, who was quoted by Reuters. Genzyme had previously said it would turn in the regulatory filing in the second half of 2010, according to the Reuters report.